parmfile (c49b1)
CHARMM Emprical Energy Function Parameters
This section describes parameters in the CHARMM empirical
energy function.
* Overview | Overview of CHARMM parameter file
* Multiple | Rules for the use of multiple dihedrals in CHARMM22
* Conversion | Rules for conversion of old nucleic acid rtf and
param to CHARMM22 format
* PARMDATA | Description of Parameter Files available for general use.
This section describes parameters in the CHARMM empirical
energy function.
* Overview | Overview of CHARMM parameter file
* Multiple | Rules for the use of multiple dihedrals in CHARMM22
* Conversion | Rules for conversion of old nucleic acid rtf and
param to CHARMM22 format
* PARMDATA | Description of Parameter Files available for general use.
Top
Overview of CHARMM parameter files
By Alexander D. MacKerell Jr., July 1997
Updated; January 2010
This section of the documenation contains a brief description
of the contents of a parameter file. The CHARMM parameter file
contains the information necessary to calculate energies etc. when
combined with the information from a PSF file for a structure.
Information on the keywords found in the parameter file is in IO.DOC.
(A) * CHARMM example parameter file
*
(B) BOND
H O 500.0 1.00
(C) ANGLe (THETa)
H O H 100.0 104.51 20.0 1.70
(D) DIHEdral (PHI)
HT CT CT HT 10.0 3 180.0
X CT CT X 10.0 3 180.0
(E) IMPH
O C CT N 5.0 1 0.0
X C CT X 5.0 1 0.0
X X CT N 5.0 1 0.0
O X X N 5.0 1 0.0
(F) CMAP
CT1 N CT1 C N CT1 C CT1 24
cmap data: 2D array of energy correction values
(G) NBONDed nonbond-spec
H 0.00 -0.046 0.2245 0.00 -0.023 0.2245
O 0.00 -0.120 1.8000 0.00 -0.060 1.8000
(H) NBFIX
H O -0.30 1.50 -0.15 1.50
(I) HBONDs hbond terms (IO.DOC)
H O -0.00 1.00
(J) END
The parameter file starts with a title (A) which contains
information on the origins and applicability of that file.
Section (B) BONDs, contains information on all bond force
constants and equilibrium geometries. In this as well as the
remainder of the parameter file the bonds etc. are specified by the
atom type associated with each IUPAC atom in the topology file.
Section (C) ANGLes or THETas, are specified by 3 atom types
followed by the force constant and equilibrium geometry. If a
Urey-Bradley term is desired between the 1 and 3 atom types of the
angle a second U-B force constant and equilibrium geometry are
included. If the equilibrium geometry is given as a negative
number, then a cosine based angle energy function is used instead of
NOT supported for the cosine based angle potential.
Section (D) DIHEdrals (PHI), contains the 4 atom types
specifing a dihedral followed by the force constant, the multiplicity
of the dihedral and the minimium geometry of the dihedral. With
dihedrals wildcards, X, as shown may be included for the terminal
atoms. Also, multiple dihedrals of different multiplicities may be
specified for a single dihedral as outlined below. As of version 25
any value of the phase (besides 0 and 180) is possible. However, the
use of phases other than 0 and 180 is discouraged, as the resulting
potential is asymmetric, and hence unphysical in most (if not all)
cases. » io for more information.
Improper dihedrals (E) IMPH, used for out of plane motions are
specified in the same fashion as dihedrals. The use of wildcards, X,
is also allowed in a number of variations. Multiple improper
dihedrals are not supported. Ordinarily, improper dihedrals are given
a multiplicity of 0, which imposes a harmonic restoring potential
instead of a cosine function. In this case, the central atom must be
either the first or the last atom in the definition, else the
resulting potential will be asymmetric and exhibit a discontinuity at
equilibrium! By convention, the first atom of an improper dihedral
(type A-X-X-B or A-B-C-D) should be the central atom. » io for
more information.
Cross-term energy correction map, CMAP (F), is a 2D grid
correction where the 2 dimensions correspond to two dihedral angles,
where the first four atom types correspond to the first dihedral and
the next four atom types to the second dihedral angle. A CMAP
specification is required in the topology file (» rtop ) and
properly generated for this energy term to be applied. The integer
following the 8 atom types represents the dimensions of the 2D grid.
In the present example, 24 indicates that for the 360x360 deg surface,
grid data in 15 deg increments is being used. The data in the CMAP
grid is presented starting from -180 down to 0 and then increased to
the final value (165 for the present example).
Parameters for (G) NONBonded VDW parameters may be specified
in two ways. Initially the Tanford-Kirkwood Formula was used where
the atom polarizabilities, Number of effective electrons, and (minimum
radius)/2 were required. In this formulation the first term following
the atom type is the atom polarizability, the second term is the
number of effective electrons and must be positive in order to specify
the Tanford-Kirkwood Formula and the third term is the (minimum
radius)/2. If the second term is negative, then the first number is
ignored, the second term is the well-depth (epsilon) and the third
term is the (minimum radius)/2. Both formulations use the
Lennard-Jones 6-12 formula to determine the VDW interactions, in the
first method the Tanford-Kirkwood Formula is used to calculate the
well-depth (epsilon) and in the second method it is used directly.
With both formulations a second set of 3 numbers may be specified to
indicate the VDW parameters to be used for the calculation of 1-4
nonbonded interactions. Wildcards (*, %, etc. see MISCOM.DOC) may be
used with the NONBond as well as the NBFIX and HBOND sections of the
parameter file.
The NBFIX section (H) allows VDW interactions between specific
atom pairs to be modified. This is done by specifing the 2 atom types
followed by the well depth and the minimum radius (not (minimum
radius)/2 as in NBOND). A second well depth and minimum radius may be
specified to determine the 1-4 interactions.
The final section (I) contains the hydogen bond well depths
and minimum radii for various atom pairs. In current versions of the
parameters) hydrogen bonding is included implicitly in the
electrostatic and VDW interactions. Thus, the HBOND well depth is set
to -0.00 and in most calculations IHBFRQ should be set to 0 to avoid
updating the hydrogen bond lists. This facility is still supported to
allow calculations using the Lennart Nilsson nucleic acid parameters,
AMBER parameters and for analysis of hydrogen bond geometries. It
should be noted that both the NBOND and HBOND keywords are followed by
a number of keywords dictating truncation schemes, 1-4 interaction
treatments and dielectric constants, amoung others. These
specifications are of the upmost importance for relabile calculations
and deviations from the default values supplied with the parameter
files should be done with the utmost caution. As of version 27, a
special parameter files, par_hbond.inp, was added to the toppar
directory; it contains information to calculated hydrogen bonds. Note
that the resulting energetics are meaningless and are only included to
aid in the analysis of hydrogen bonds.
Overview of CHARMM parameter files
By Alexander D. MacKerell Jr., July 1997
Updated; January 2010
This section of the documenation contains a brief description
of the contents of a parameter file. The CHARMM parameter file
contains the information necessary to calculate energies etc. when
combined with the information from a PSF file for a structure.
Information on the keywords found in the parameter file is in IO.DOC.
(A) * CHARMM example parameter file
*
(B) BOND
H O 500.0 1.00
(C) ANGLe (THETa)
H O H 100.0 104.51 20.0 1.70
(D) DIHEdral (PHI)
HT CT CT HT 10.0 3 180.0
X CT CT X 10.0 3 180.0
(E) IMPH
O C CT N 5.0 1 0.0
X C CT X 5.0 1 0.0
X X CT N 5.0 1 0.0
O X X N 5.0 1 0.0
(F) CMAP
CT1 N CT1 C N CT1 C CT1 24
cmap data: 2D array of energy correction values
(G) NBONDed nonbond-spec
H 0.00 -0.046 0.2245 0.00 -0.023 0.2245
O 0.00 -0.120 1.8000 0.00 -0.060 1.8000
(H) NBFIX
H O -0.30 1.50 -0.15 1.50
(I) HBONDs hbond terms (IO.DOC)
H O -0.00 1.00
(J) END
The parameter file starts with a title (A) which contains
information on the origins and applicability of that file.
Section (B) BONDs, contains information on all bond force
constants and equilibrium geometries. In this as well as the
remainder of the parameter file the bonds etc. are specified by the
atom type associated with each IUPAC atom in the topology file.
Section (C) ANGLes or THETas, are specified by 3 atom types
followed by the force constant and equilibrium geometry. If a
Urey-Bradley term is desired between the 1 and 3 atom types of the
angle a second U-B force constant and equilibrium geometry are
included. If the equilibrium geometry is given as a negative
number, then a cosine based angle energy function is used instead of
NOT supported for the cosine based angle potential.
Section (D) DIHEdrals (PHI), contains the 4 atom types
specifing a dihedral followed by the force constant, the multiplicity
of the dihedral and the minimium geometry of the dihedral. With
dihedrals wildcards, X, as shown may be included for the terminal
atoms. Also, multiple dihedrals of different multiplicities may be
specified for a single dihedral as outlined below. As of version 25
any value of the phase (besides 0 and 180) is possible. However, the
use of phases other than 0 and 180 is discouraged, as the resulting
potential is asymmetric, and hence unphysical in most (if not all)
cases. » io for more information.
Improper dihedrals (E) IMPH, used for out of plane motions are
specified in the same fashion as dihedrals. The use of wildcards, X,
is also allowed in a number of variations. Multiple improper
dihedrals are not supported. Ordinarily, improper dihedrals are given
a multiplicity of 0, which imposes a harmonic restoring potential
instead of a cosine function. In this case, the central atom must be
either the first or the last atom in the definition, else the
resulting potential will be asymmetric and exhibit a discontinuity at
equilibrium! By convention, the first atom of an improper dihedral
(type A-X-X-B or A-B-C-D) should be the central atom. » io for
more information.
Cross-term energy correction map, CMAP (F), is a 2D grid
correction where the 2 dimensions correspond to two dihedral angles,
where the first four atom types correspond to the first dihedral and
the next four atom types to the second dihedral angle. A CMAP
specification is required in the topology file (» rtop ) and
properly generated for this energy term to be applied. The integer
following the 8 atom types represents the dimensions of the 2D grid.
In the present example, 24 indicates that for the 360x360 deg surface,
grid data in 15 deg increments is being used. The data in the CMAP
grid is presented starting from -180 down to 0 and then increased to
the final value (165 for the present example).
Parameters for (G) NONBonded VDW parameters may be specified
in two ways. Initially the Tanford-Kirkwood Formula was used where
the atom polarizabilities, Number of effective electrons, and (minimum
radius)/2 were required. In this formulation the first term following
the atom type is the atom polarizability, the second term is the
number of effective electrons and must be positive in order to specify
the Tanford-Kirkwood Formula and the third term is the (minimum
radius)/2. If the second term is negative, then the first number is
ignored, the second term is the well-depth (epsilon) and the third
term is the (minimum radius)/2. Both formulations use the
Lennard-Jones 6-12 formula to determine the VDW interactions, in the
first method the Tanford-Kirkwood Formula is used to calculate the
well-depth (epsilon) and in the second method it is used directly.
With both formulations a second set of 3 numbers may be specified to
indicate the VDW parameters to be used for the calculation of 1-4
nonbonded interactions. Wildcards (*, %, etc. see MISCOM.DOC) may be
used with the NONBond as well as the NBFIX and HBOND sections of the
parameter file.
The NBFIX section (H) allows VDW interactions between specific
atom pairs to be modified. This is done by specifing the 2 atom types
followed by the well depth and the minimum radius (not (minimum
radius)/2 as in NBOND). A second well depth and minimum radius may be
specified to determine the 1-4 interactions.
The final section (I) contains the hydogen bond well depths
and minimum radii for various atom pairs. In current versions of the
parameters) hydrogen bonding is included implicitly in the
electrostatic and VDW interactions. Thus, the HBOND well depth is set
to -0.00 and in most calculations IHBFRQ should be set to 0 to avoid
updating the hydrogen bond lists. This facility is still supported to
allow calculations using the Lennart Nilsson nucleic acid parameters,
AMBER parameters and for analysis of hydrogen bond geometries. It
should be noted that both the NBOND and HBOND keywords are followed by
a number of keywords dictating truncation schemes, 1-4 interaction
treatments and dielectric constants, amoung others. These
specifications are of the upmost importance for relabile calculations
and deviations from the default values supplied with the parameter
files should be done with the utmost caution. As of version 27, a
special parameter files, par_hbond.inp, was added to the toppar
directory; it contains information to calculated hydrogen bonds. Note
that the resulting energetics are meaningless and are only included to
aid in the analysis of hydrogen bonds.
Top
Rules for the use of multiple dihedrals in CHARMM24
1) The association of 1 or more dihedrals with different
multiplicities to a specfic dihedral type (as specified
by atom types) is specified by the presence of 2 or
more dihedral parameters in the parameter file. When
multiple dihedrals are read in the parameter file and if the
warning level (wrnlev) is 6 or more CHARMM
will list those dihedrals in the output file (Note: the following
type message "PARRDR> Multiple terms for dihedral type: INDEX 427
CODE31141959 CT3 -OS -CD -OB" indicates that the multiple
dihedral has been successfully read).
2) If dihedral angles are AUTOGENERATED, then the RTF should
not specify them again. Additional dihedrals in the RTF will
be ignored and warnings given.
3) Without AUTOGENERATE, each dihedral should appear only once
in the RTF. Multiple listings of a dihedral will be ignored
and warnings given.
4) The order of the multiple dihedral entries associated with
a specific dihedral is important; they must be placed
sequentially in the parameter file. If they are not sequential
errors will be given. This is new in C24B1 and later versions.
For example:
P ON2 P2 ON2 0.03 2 0.0
P ON2 P2 ON2 0.03 3 0.0
will place both a 2-fold and a 3-fold term on the P-ON2-P2-ON2
dihedral.
5) Wildcards may be used in the parameter file to specify multiple
dihedrals(ie. X C1 C2 X), however, all the dihedrals in the
parameter file associated with that dihedral type must be
wildcards. Use of wildcards with multiple dihedrals is NOT
recommeded.
6) Specific dihedral entries always override wildcard entries.
For example:
X C2 C3 X 100.0 1 180.0
C1 C2 C3 C4 100.0 2 180.0
X C2 C3 X 100.0 3 180.0
will assign the 2-fold term to C1-C2-C3-C4 while 1-fold and
3-fold terms would be assigned to C5-C2-C3-C6 and any other
dihedral centered about the C2-C3 bond. This assignment of
the multiple terms to a number of dihedrals is why the use
wildcards for the specification of multiple dihedrals in NOT
recommeded. The preferred method is as follows:
X C2 C3 X 100.0 2 180.0
C5 C2 C3 C6 100.0 1 180.0
C5 C2 C3 C6 100.0 3 180.0
will assign the 1-fold and 3-fold terms to C5-C2-C3-C6 and the
2-fold term to C1-C2-C3-C4 and any other dihedral centered about
the C2-C3 bond. This limits the potential for multiple dihedrals
being mistakenly assigned to a dihedral centered on the C2-C3 bond.
Thus, it is advised that when creating a multiple dihedral all
4 atom types be explicitly stated and, if necessary, new atom
types be created to avoid conflicts.
7) This design is such that previous CHARMM topology and parameter
files for proteins are compatible with CHARMM24. However, due
to complexities in the multiple dihedral setup for the nucleic
acid sugars (ribose and deoxyribose) the nucleic acid topology
and parameter files are NOT compatible with CHARMM22. In order
to make them compatible the following alterations must be
performed. Alternatively, the altered files may be obained
from Alexander D. MacKerell Jr.
Rules for the use of multiple dihedrals in CHARMM24
1) The association of 1 or more dihedrals with different
multiplicities to a specfic dihedral type (as specified
by atom types) is specified by the presence of 2 or
more dihedral parameters in the parameter file. When
multiple dihedrals are read in the parameter file and if the
warning level (wrnlev) is 6 or more CHARMM
will list those dihedrals in the output file (Note: the following
type message "PARRDR> Multiple terms for dihedral type: INDEX 427
CODE31141959 CT3 -OS -CD -OB" indicates that the multiple
dihedral has been successfully read).
2) If dihedral angles are AUTOGENERATED, then the RTF should
not specify them again. Additional dihedrals in the RTF will
be ignored and warnings given.
3) Without AUTOGENERATE, each dihedral should appear only once
in the RTF. Multiple listings of a dihedral will be ignored
and warnings given.
4) The order of the multiple dihedral entries associated with
a specific dihedral is important; they must be placed
sequentially in the parameter file. If they are not sequential
errors will be given. This is new in C24B1 and later versions.
For example:
P ON2 P2 ON2 0.03 2 0.0
P ON2 P2 ON2 0.03 3 0.0
will place both a 2-fold and a 3-fold term on the P-ON2-P2-ON2
dihedral.
5) Wildcards may be used in the parameter file to specify multiple
dihedrals(ie. X C1 C2 X), however, all the dihedrals in the
parameter file associated with that dihedral type must be
wildcards. Use of wildcards with multiple dihedrals is NOT
recommeded.
6) Specific dihedral entries always override wildcard entries.
For example:
X C2 C3 X 100.0 1 180.0
C1 C2 C3 C4 100.0 2 180.0
X C2 C3 X 100.0 3 180.0
will assign the 2-fold term to C1-C2-C3-C4 while 1-fold and
3-fold terms would be assigned to C5-C2-C3-C6 and any other
dihedral centered about the C2-C3 bond. This assignment of
the multiple terms to a number of dihedrals is why the use
wildcards for the specification of multiple dihedrals in NOT
recommeded. The preferred method is as follows:
X C2 C3 X 100.0 2 180.0
C5 C2 C3 C6 100.0 1 180.0
C5 C2 C3 C6 100.0 3 180.0
will assign the 1-fold and 3-fold terms to C5-C2-C3-C6 and the
2-fold term to C1-C2-C3-C4 and any other dihedral centered about
the C2-C3 bond. This limits the potential for multiple dihedrals
being mistakenly assigned to a dihedral centered on the C2-C3 bond.
Thus, it is advised that when creating a multiple dihedral all
4 atom types be explicitly stated and, if necessary, new atom
types be created to avoid conflicts.
7) This design is such that previous CHARMM topology and parameter
files for proteins are compatible with CHARMM24. However, due
to complexities in the multiple dihedral setup for the nucleic
acid sugars (ribose and deoxyribose) the nucleic acid topology
and parameter files are NOT compatible with CHARMM22. In order
to make them compatible the following alterations must be
performed. Alternatively, the altered files may be obained
from Alexander D. MacKerell Jr.
Top
Rules for conversion of old nucleic acid rtf and param to CHARMM22 format
The following conversion rules apply to CHARMM22. Compatability with
C24B1 and later versions will be insured if the multiple dihedrals in
the converted parameters are sequential, as disscused above.
ALL-HYDROGEN
Protocol for conversion of all-hydrogen nucleic acid topology and
parameter files (topnah*.inp and parnah*.inp) from a CHARMM21 or
previous format to a format compatible with CHARMM22. This change is
due to a new methodology for the treatment of multiple dihedrals in
In Topology File (TOPNAH1.INP, TOPNAH1E.INP, TOPNAH1R.INP)
1) Create a new atom type, OSS
2) Convert the atom type of all O4' atoms to OSS
In Parameter File (PARNAH1.INP)
1) Copy all OS parameters (bonds, angles, dihedrals etc.)
and in the copy change OS to OSS. Be sure that the
original OS parameter remains. Some OS to OSS copies
can be avoided (such as OS P terms), however, one
must be careful that all the necessary OSS parameters
relating to O4' are present. Creating extra OSS
parameters which are unused is not a problem. One
exception occurs with the dihedral OS CH CH OS, where
only one of the terminal OS atom should be converted
to OSS.
2) In the DIHEDRAL (PHI) parameters under the heading
"WILMA OLSON SUGAR MODEL" the following steps must be
performed once all the OSS dihedral parameters are
created.
A) In all the explicit OS terms which don't include
wildcards (X) or P atom types and have both 2 and
3-fold periodicities (2nd of 3 numbers following the
dihedral) the 2nd 3-fold term must be commented out
with a !.
B) Of the new explicit OSS terms the following
3-fold terms must be commented out with a !.
OSS CH CH OS 1.4000 3 0.0000
OH CH CH OSS 1.4000 3 0.0000
Lastly, when generating the structure be sure only the AUTOGENERATE
ANGLE term is used. (i.e. do NOT use AUTOGENERATE DIHEDRAL).
At this point the topology and parameter files should be
compatible with CHARMM22 (but not CHARMM21 or a previous version of
containing compound. In this test the energies should be calculated
1) using CHARMM21 or a previous version using the original, unmodified
topology and parameter files and 2) with CHARMM22 using the modified
OSS containing topology and parameter files. These energies should be
equivalent.
EXTENDED (UNITED) ATOM
Protocal for the conversion of extended (united,explicit) atom
nucleic acid topology and parameter files from CHARMM21 or previous
format to a format compatible with CHARMM22. This change is due to a
new methodology for the treatment of multiple dihedrals in CHARMM22.
In Topology File (TOPRNA10 or TOPRNA10R)
1) Create 2 new atom types, OSS and OST
2) Convert the atom type of all O4' atoms to OSS except
in the the patch PRES DEOX where it must be changed
to atom type OST. This conversion to OST must also be
performed in any residue, such as RESI DRIB, in which
deoxyribose is used explicitly.
3) In the patch PRES DEOX add the line:
ATOM O4' OST -0.30 ! (check the charge)
before the GROUP statement and comment out the terms
!DELETE DIHE O4' C4' C3' O3' ! WE NEED THIS AS A MULTIPLE TERM IN DEOXY
!DIHE O4' C4' C3' O3' ! threefold
!DIHE O4' C4' C3' O3' ! twofold
such that no alterations in the dihedral setup are made.
In Parameter File (PARDNA10.INP)
1) Copy all OS parameters twice (bonds, angles, dihedrals etc.);
in the first copy change OS to OSS and in the second change OS
to OST. Be sure that the original OS parameter remains. Some
OS to OSS(OST) copies can be avoided (such as terms in which OS
is adjacent to P), however, one must be careful that all the
necessary OSS(OST) parameters relating to O4' are present.
Creating extra OSS(OST) parameters which are unused is not a
problem. One exception occurs with the dihedral OS CH CH OS,
where only one of the terminal OS atom should be converted
to OSS(OST).
2) In the DIHEDRAL (PHI) parameters under the heading
"WILMA OLSON SUGAR MODEL" the following steps must be
performed once all the OSS(OST) dihedral parameters are
created.
A) In all the explicit OS terms which don't include
wildcards (X) or P atom types and have both 2 and
3-fold periodicities (2nd of 3 numbers following the
dihedral) the 2nd term must be commented out
with a ! (mostly 3-fold terms and 1 or 2 2-fold term).
B) Of the new explicit OSS terms the following
3-fold terms must be commented out with a !.
OSS CH CH OS 1.4000 3 0.0000
OH CH CH OSS 1.4000 3 0.0000
C) Maintain all of the OST dihedral terms.
An example of the additions/alterations to pardna10.inp are
listed below.
BOND
HO OSS 450.0000 0.9600
HO OST 450.0000 0.9600
OSS CH 292.0000 1.4300
OSS C2 292.0000 1.4300
OST CH 292.0000 1.4300
OST C2 292.0000 1.4300
C3 OSS 292.0000 1.38
C3 OST 292.0000 1.38
C OSS 292.0000 1.43
C OST 292.0000 1.43
THETA
OSS C2 C3 150.5000 111.0000
OSS C2 CH 70.0000 112.0000
OSS C2 C2 82.0000 112.0000
OST C2 C3 150.5000 111.0000
OST C2 CH 70.0000 112.0000
OST C2 C2 82.0000 112.0000
C2 CH OSS 46.5000 111.0000
C2 CH OST 46.5000 111.0000
C3 CH OSS 46.5000 111.0000
C3 CH OST 46.5000 111.0000
CH CH OSS 46.5000 111.0000
CH CH OST 46.5000 111.0000
OSS CH NS 46.5000 111.0000
OSS CH NH2E 46.5000 111.0000
OST CH NS 46.5000 111.0000
OST CH NH2E 46.5000 111.0000
C2 OSS C2 82.0000 111.5000
CH OSS CH 46.5000 111.5000
HO OSS CH 46.5000 107.3000
HO OSS C2 46.5000 107.3000
C2 OST C2 82.0000 111.5000
CH OST CH 46.5000 111.5000
HO OST CH 46.5000 107.3000
HO OST C2 46.5000 107.3000
CH OSS C3 46.5 107.3
CH OST C3 46.5 107.3
C OSS C3 46.5 120.5
C OST C3 46.5 120.5
O C OSS 70.0 120.0
O C OST 70.0 120.0
CH C OSS 70.0 125.3
NA C OSS 70.0 120.0
CH C OST 70.0 125.3
NA C OST 70.0 120.0
OSS CH CS 46.5 111.0
OST CH CS 46.5 111.0
PHI
X CH OSS X 0.9000 3 0.0000
X CH OST X 0.9000 3 0.0000
X C2 OSS X 0.5000 3 0.0000
X C2 OST X 0.5000 3 0.0000
! OSS SUGAR TERMS
OSS CH CH OS 0.5000 2 0.0000
!OSS CH CH OS 1.4000 3 0.0000 Should be commented out
OH CH CH OSS 0.5000 2 0.0000
!OH CH CH OSS 1.4000 3 0.0000 Should be commented out
OSS CH CH CH 0.5000 2 0.0000
OSS CH CH CH 1.4000 3 0.0000
OSS CH C2 CH 1.0000 2 0.0000
OSS CH C2 CH 1.4000 3 0.0000
OSS CH CH C2 1.4000 3 0.0000
OSS CH CH C2 0.5000 2 0.0000
OSS C2 C2 C2 1.4 3 0.0
OSS C2 C2 C2 0.5 2 0.0
! OST SUGAR TERMS
OST CH CH OS 0.5000 2 0.0000
OST CH CH OS 1.4000 3 0.0000
OH CH CH OST 0.5000 2 0.0000
OH CH CH OST 1.4000 3 0.0000
OST CH CH CH 0.5000 2 0.0000
OST CH CH CH 1.4000 3 0.0000
OST CH C2 CH 1.0000 2 0.0000
OST CH C2 CH 1.4000 3 0.0000
OST CH CH C2 1.4000 3 0.0000
OST CH CH C2 0.5000 2 0.0000
OST C2 C2 C2 1.4 3 0.0
OST C2 C2 C2 0.5 2 0.0
! additional terms for tRNA
OSS CH CS CF 1.5 3 0.0
OST CH CS CF 1.5 3 0.0
C2 CH C OSS 1.5 3 0.0
C2 CH C OST 1.5 3 0.0
X C OSS X 1.8 2 180.00
X C OST X 1.8 2 180.00
! THE FOLLOWING TERMS UNDER THE HEADER
! "WILMA OLSON SUGAR MODEL":
! SHOULD BE COMMENTED OUT
!OS CH CH OS 1.4000 3 0.0000
!OS CH CH CH 1.4000 3 0.0000
!OH CH CH OS 1.4000 3 0.0000
!OS CH C2 CH 1.4000 3 0.0000
!OS CH CH C2 0.5000 2 0.0000
!OS C2 C2 C2 0.5 2 0.0
IMPHI
OSS X X CH 31.5000 0 35.2600
OST X X CH 31.5000 0 35.2600
CH OSS C2 NS 31.5000 0 35.2600
CH OSS CH NS 31.5000 0 35.2600
CH OSS C2 NH2E 31.5000 0 35.2600
CH OSS CH NH2E 31.5000 0 35.2600
CH OST C2 NS 31.5000 0 35.2600
CH OST CH NS 31.5000 0 35.2600
CH OST C2 NH2E 31.5000 0 35.2600
CH OST CH NH2E 31.5000 0 35.2600
NBONDED
OSS 0.64 7.0 1.6
OST 0.64 7.0 1.6
Lastly, when generating the structure be sure only the
AUTOGENERATE ANGLE term is used. (i.e. do NOT use AUTOGENERATE
DIHEDRAL).
At this point the topology and parameter files should be
compatible with CHARMM22 (but not CHARMM21 or a previous version of
containing compound. In this test the energies should be calculated
1) using CHARMM21 or a previous version using the original, unmodified
topology and parameter files and 2) with CHARMM22 using the modified
OSS containing topology and parameter files. These energies should be
equivalent.
Rules for conversion of old nucleic acid rtf and param to CHARMM22 format
The following conversion rules apply to CHARMM22. Compatability with
C24B1 and later versions will be insured if the multiple dihedrals in
the converted parameters are sequential, as disscused above.
ALL-HYDROGEN
Protocol for conversion of all-hydrogen nucleic acid topology and
parameter files (topnah*.inp and parnah*.inp) from a CHARMM21 or
previous format to a format compatible with CHARMM22. This change is
due to a new methodology for the treatment of multiple dihedrals in
In Topology File (TOPNAH1.INP, TOPNAH1E.INP, TOPNAH1R.INP)
1) Create a new atom type, OSS
2) Convert the atom type of all O4' atoms to OSS
In Parameter File (PARNAH1.INP)
1) Copy all OS parameters (bonds, angles, dihedrals etc.)
and in the copy change OS to OSS. Be sure that the
original OS parameter remains. Some OS to OSS copies
can be avoided (such as OS P terms), however, one
must be careful that all the necessary OSS parameters
relating to O4' are present. Creating extra OSS
parameters which are unused is not a problem. One
exception occurs with the dihedral OS CH CH OS, where
only one of the terminal OS atom should be converted
to OSS.
2) In the DIHEDRAL (PHI) parameters under the heading
"WILMA OLSON SUGAR MODEL" the following steps must be
performed once all the OSS dihedral parameters are
created.
A) In all the explicit OS terms which don't include
wildcards (X) or P atom types and have both 2 and
3-fold periodicities (2nd of 3 numbers following the
dihedral) the 2nd 3-fold term must be commented out
with a !.
B) Of the new explicit OSS terms the following
3-fold terms must be commented out with a !.
OSS CH CH OS 1.4000 3 0.0000
OH CH CH OSS 1.4000 3 0.0000
Lastly, when generating the structure be sure only the AUTOGENERATE
ANGLE term is used. (i.e. do NOT use AUTOGENERATE DIHEDRAL).
At this point the topology and parameter files should be
compatible with CHARMM22 (but not CHARMM21 or a previous version of
containing compound. In this test the energies should be calculated
1) using CHARMM21 or a previous version using the original, unmodified
topology and parameter files and 2) with CHARMM22 using the modified
OSS containing topology and parameter files. These energies should be
equivalent.
EXTENDED (UNITED) ATOM
Protocal for the conversion of extended (united,explicit) atom
nucleic acid topology and parameter files from CHARMM21 or previous
format to a format compatible with CHARMM22. This change is due to a
new methodology for the treatment of multiple dihedrals in CHARMM22.
In Topology File (TOPRNA10 or TOPRNA10R)
1) Create 2 new atom types, OSS and OST
2) Convert the atom type of all O4' atoms to OSS except
in the the patch PRES DEOX where it must be changed
to atom type OST. This conversion to OST must also be
performed in any residue, such as RESI DRIB, in which
deoxyribose is used explicitly.
3) In the patch PRES DEOX add the line:
ATOM O4' OST -0.30 ! (check the charge)
before the GROUP statement and comment out the terms
!DELETE DIHE O4' C4' C3' O3' ! WE NEED THIS AS A MULTIPLE TERM IN DEOXY
!DIHE O4' C4' C3' O3' ! threefold
!DIHE O4' C4' C3' O3' ! twofold
such that no alterations in the dihedral setup are made.
In Parameter File (PARDNA10.INP)
1) Copy all OS parameters twice (bonds, angles, dihedrals etc.);
in the first copy change OS to OSS and in the second change OS
to OST. Be sure that the original OS parameter remains. Some
OS to OSS(OST) copies can be avoided (such as terms in which OS
is adjacent to P), however, one must be careful that all the
necessary OSS(OST) parameters relating to O4' are present.
Creating extra OSS(OST) parameters which are unused is not a
problem. One exception occurs with the dihedral OS CH CH OS,
where only one of the terminal OS atom should be converted
to OSS(OST).
2) In the DIHEDRAL (PHI) parameters under the heading
"WILMA OLSON SUGAR MODEL" the following steps must be
performed once all the OSS(OST) dihedral parameters are
created.
A) In all the explicit OS terms which don't include
wildcards (X) or P atom types and have both 2 and
3-fold periodicities (2nd of 3 numbers following the
dihedral) the 2nd term must be commented out
with a ! (mostly 3-fold terms and 1 or 2 2-fold term).
B) Of the new explicit OSS terms the following
3-fold terms must be commented out with a !.
OSS CH CH OS 1.4000 3 0.0000
OH CH CH OSS 1.4000 3 0.0000
C) Maintain all of the OST dihedral terms.
An example of the additions/alterations to pardna10.inp are
listed below.
BOND
HO OSS 450.0000 0.9600
HO OST 450.0000 0.9600
OSS CH 292.0000 1.4300
OSS C2 292.0000 1.4300
OST CH 292.0000 1.4300
OST C2 292.0000 1.4300
C3 OSS 292.0000 1.38
C3 OST 292.0000 1.38
C OSS 292.0000 1.43
C OST 292.0000 1.43
THETA
OSS C2 C3 150.5000 111.0000
OSS C2 CH 70.0000 112.0000
OSS C2 C2 82.0000 112.0000
OST C2 C3 150.5000 111.0000
OST C2 CH 70.0000 112.0000
OST C2 C2 82.0000 112.0000
C2 CH OSS 46.5000 111.0000
C2 CH OST 46.5000 111.0000
C3 CH OSS 46.5000 111.0000
C3 CH OST 46.5000 111.0000
CH CH OSS 46.5000 111.0000
CH CH OST 46.5000 111.0000
OSS CH NS 46.5000 111.0000
OSS CH NH2E 46.5000 111.0000
OST CH NS 46.5000 111.0000
OST CH NH2E 46.5000 111.0000
C2 OSS C2 82.0000 111.5000
CH OSS CH 46.5000 111.5000
HO OSS CH 46.5000 107.3000
HO OSS C2 46.5000 107.3000
C2 OST C2 82.0000 111.5000
CH OST CH 46.5000 111.5000
HO OST CH 46.5000 107.3000
HO OST C2 46.5000 107.3000
CH OSS C3 46.5 107.3
CH OST C3 46.5 107.3
C OSS C3 46.5 120.5
C OST C3 46.5 120.5
O C OSS 70.0 120.0
O C OST 70.0 120.0
CH C OSS 70.0 125.3
NA C OSS 70.0 120.0
CH C OST 70.0 125.3
NA C OST 70.0 120.0
OSS CH CS 46.5 111.0
OST CH CS 46.5 111.0
PHI
X CH OSS X 0.9000 3 0.0000
X CH OST X 0.9000 3 0.0000
X C2 OSS X 0.5000 3 0.0000
X C2 OST X 0.5000 3 0.0000
! OSS SUGAR TERMS
OSS CH CH OS 0.5000 2 0.0000
!OSS CH CH OS 1.4000 3 0.0000 Should be commented out
OH CH CH OSS 0.5000 2 0.0000
!OH CH CH OSS 1.4000 3 0.0000 Should be commented out
OSS CH CH CH 0.5000 2 0.0000
OSS CH CH CH 1.4000 3 0.0000
OSS CH C2 CH 1.0000 2 0.0000
OSS CH C2 CH 1.4000 3 0.0000
OSS CH CH C2 1.4000 3 0.0000
OSS CH CH C2 0.5000 2 0.0000
OSS C2 C2 C2 1.4 3 0.0
OSS C2 C2 C2 0.5 2 0.0
! OST SUGAR TERMS
OST CH CH OS 0.5000 2 0.0000
OST CH CH OS 1.4000 3 0.0000
OH CH CH OST 0.5000 2 0.0000
OH CH CH OST 1.4000 3 0.0000
OST CH CH CH 0.5000 2 0.0000
OST CH CH CH 1.4000 3 0.0000
OST CH C2 CH 1.0000 2 0.0000
OST CH C2 CH 1.4000 3 0.0000
OST CH CH C2 1.4000 3 0.0000
OST CH CH C2 0.5000 2 0.0000
OST C2 C2 C2 1.4 3 0.0
OST C2 C2 C2 0.5 2 0.0
! additional terms for tRNA
OSS CH CS CF 1.5 3 0.0
OST CH CS CF 1.5 3 0.0
C2 CH C OSS 1.5 3 0.0
C2 CH C OST 1.5 3 0.0
X C OSS X 1.8 2 180.00
X C OST X 1.8 2 180.00
! THE FOLLOWING TERMS UNDER THE HEADER
! "WILMA OLSON SUGAR MODEL":
! SHOULD BE COMMENTED OUT
!OS CH CH OS 1.4000 3 0.0000
!OS CH CH CH 1.4000 3 0.0000
!OH CH CH OS 1.4000 3 0.0000
!OS CH C2 CH 1.4000 3 0.0000
!OS CH CH C2 0.5000 2 0.0000
!OS C2 C2 C2 0.5 2 0.0
IMPHI
OSS X X CH 31.5000 0 35.2600
OST X X CH 31.5000 0 35.2600
CH OSS C2 NS 31.5000 0 35.2600
CH OSS CH NS 31.5000 0 35.2600
CH OSS C2 NH2E 31.5000 0 35.2600
CH OSS CH NH2E 31.5000 0 35.2600
CH OST C2 NS 31.5000 0 35.2600
CH OST CH NS 31.5000 0 35.2600
CH OST C2 NH2E 31.5000 0 35.2600
CH OST CH NH2E 31.5000 0 35.2600
NBONDED
OSS 0.64 7.0 1.6
OST 0.64 7.0 1.6
Lastly, when generating the structure be sure only the
AUTOGENERATE ANGLE term is used. (i.e. do NOT use AUTOGENERATE
DIHEDRAL).
At this point the topology and parameter files should be
compatible with CHARMM22 (but not CHARMM21 or a previous version of
containing compound. In this test the energies should be calculated
1) using CHARMM21 or a previous version using the original, unmodified
topology and parameter files and 2) with CHARMM22 using the modified
OSS containing topology and parameter files. These energies should be
equivalent.
Top
Description of topology and parameter files in version c31 and
subsequent versions.
In version 31 a major restructuring of the topology and parameter
files was undertaken. This was performed to create a more modular
approach to the files, thereby avoiding the problem of files becoming
increasingly large. The restructuring was done such that the primary
topology and parameter files for biomolecules can be used as they were
previously. However, the topology and parameter information for the
majority of model compounds used in the parameter development,
additional molecules, including coenzymes, and patches parametrized to
be compatible with the CHARMM force fields have been moved to toppar
stream files. These toppar stream files have to be streamed in a
and parameter files. They include both the topology and parameter
information for the selected molecules, using the "read rtf card
append" and "read param card append" commands to append the additional
information to the topology and parameter lists. As of version c31 it
is still necessary to maintain all the MASS atom lists in the parent
topology and parameter files.
Files in Version C35/C36
Topology files
top_all22_prot.inp all hydrogen RTF for proteins, CHARMM22 with CMAP
top_all35_carb.rtf all hydrogen RTF for sugars
top_all32_lipid.rtf all hydrogen RTF for lipids with alkane dihedral update
top_all36_lipid.rtf all hydrogen RTF for lipids (C36 and on)
top_all27_na.rtf all hydrogen RTF for nucleic acids
top_all32_na_lipid.rtf all hydrogen RTF for nucleic acids and lipids
top_all36_na_lipid.rtf all hydrogen RTF for nucleic acids and lipids (C36 and on)
top_all27_prot_na.rtf all hydrogen RTF for proteins and nucleic acids
top_all32_prot_lipid.rtf all hydrogen RTF for proteins and lipids
top_all36_prot_lipid.rtf all hydrogen RTF for proteins and lipids (C36 and on)
top_all35_ethers.rtf all hydrogen RTF for ethers
top_all30_cheq_prot.inp all hydrogen RTF for protein charge equilibration polarizable model
toph19.inp extended atom RTF for proteins
toprna10r_22.inp extended atom RTF for nucleic acids
Parameter files
par_all22_prot.inp all hydrogen parameters for proteins with CMAP
par_all35_carb.prm all hydrogen parameters for sugars
par_all32_lipid.prm all hydrogen parameters for lipids with alkane dihedral update
par_all36_lipid.prm all hydrogen parameters for lipids (C36 and on)
par_all27_na.prm all hydrogen parameters for nucleic acids
par_all32_na_lipid.prm all hydrogen parameters for nucleic acids and lipids
par_all36_na_lipid.prm all hydrogen parameters for nucleic acids and lipids (C36 and on)
par_all27_prot_na.prm all hydrogen parameters for proteins and nucleic acids
par_all32_prot_lipid.prm all hydrogen parameters for proteins and lipids
par_all36_prot_lipid.prm all hydrogen parameters for proteins and lipids (C36 and on)
par_all30_cheq_prot.inp all hydrogen parameters for protein charge equilibration polarizable model
par_all35_ethers.prm all hydrogen parameters for ethers
param19.inp extended atom parameters for proteins
pardna10_22.inp extended atom parameters for nucleic acids
(C) Toppar stream files (see stream subdirectory) listed under the parent
topology and parameter files required for the individual files.
Parent files: can be used with prot, na and lipid files
toppar_dum_nobel_gases.str: dummy atom, helium and neon
toppar_hbond.str: stream file to estimate hydrogen bond interactions
Parent files: top_all22_prot.inp, par_all22_prot.inp
(or top_all22_prot_cmap.inp, par_all22_prot_cmap.inp)
toppar_all22_prot_model.str: model compounds used in protein parameter development
as well as additional compounds
toppar_all22_prot_aldehydes.str: small molecule aldehydes
toppar_all22_prot_aliphatic_c27.str: extends all22 protein force field to include
all27 alkane parameters
toppar_all22_prot_fluoro_alkanes.str: optimized fluoroalkanes, requires
toppar_all22_prot_aliphatic_c27.str
toppar_all22_prot_heme.str: heme, O2, CO, CO2 and related patches
toppar_all22_prot_pyridines.str: various substituted pyridines
toppar_all22_prot_retinol.str: retinol, model compounds, Schiff's bases
Parent files: top_all27_na.rtf, par_all27_na.prm
toppar_all27_na_model.str: model compounds used in na parameter development including
individual bases etc.
toppar_all27_na_base_modifications.str: various chemical modifications of bases
toppar_all27_na_carbocyclic.str: constrained bicyclic sugars
toppar_all27_na_nad_ppi.str: NAD, NADH, ADP, ATP and others. Useful in combination with
protein force field via the top_all27_prot_na.rtf
and par_all27_prot_na.prm
Parent files: top_all32_lipid.rtf, par_all32_lipid.prm
toppar_all27_lipid_model.str: model compounds used in lipid parameter development, including
alkenes
toppar_all27_lipid_cholesterol.str: cholesterol and related model compounds
Parent files: top_all36_lipid.rtf, par_all36_lipid.prm
toppar_all36_lipid_model.str: model compounds used in lipid parameter development, including
alkenes
toppar_all36_lipid_cholesterol.str: cholesterol and related model compounds
Parent files: top_all27_prot_na.rtf, par_all27_prot_na.prm
toppar_prot_na_all.str: all compounds that require both protein and nucleic acid toppar information
includes phosphorylated tyrosine, serine and threonine and some
coenzymes (SAH)
toppar_all27_na_bkb_modifications.str: various chemical modificaiton of the na backbone
including abasic variants and phosphoramidate
Parent files not needed
toppar_water_ions.str: contains TIP3P water model and ions. All of these
are also included in the prot, na and lipid topology
and parameter files.
toppar_amines.str: highly optimized neutral aliphatic amines.
(D) Parameters for the polarizable force field based on a classical
Drude oscillator. As this force field is currently under development
such that the parameters have been placed in the "drude" subdirectory.
Parameters for water, alkanes, ethers, aromatics, alcohols and amides
are available as of January 2007 and this list will be expanding. See
the 00readme for details and the approriate references.
(E) Parameters for selected silicate and aluminosilicate surfaces have
been developed. These parameters are designed to be compatible with
the CHARMM22 and 27 force fields allowing for biological
molecule-silicate surface interactions. As use of these parameters
requires creation of the surface, which entails creation of the
necessary patches, the parameters are included in the "silicates"
subdirectory. This directory also includes examples and code to
create the extended surfaces. See the 00readme file for more details.
ref: Lopes, P.E.M., Murashov, V. Tazi, M. Demchuk, E. MacKerell,
A. D., Jr. "Development of an Empirical Force Field for
Silica. Application to the Quartz-Water Interface," Journal of
Physical Chemistry B, 110: 2782-2792, 2006.
(F) Additional topology and parameter files from various sources are
included in subdirectories of the toppar directory. A description
follows:
non_charmm: Contains toppar files for AMBER, Bristol-Myers Squibb
(BMS) and OPLS force fields along with a stream file for the SPC and
SPC/E water models. These files have been tested to the extent that
they may be considered reliable representations of the original force
fields, though potentially not exact representations. These files are
NOT maintained and, thus, use at your own risk. See the 00readme
files and note that AMBER requires a special version of CHARMM as
described in the 00readme file.
tamdfff: An internal coordinate force field (ICFF) that was built
based on the CHARMM 22 protein force field. Specifically, it provides
a backbone covalent geometry suitable for torsion angle molecular
dynamics (TAMD) and the necessary CMAP cross-term corrections to
suppress distortions of the potential energy surface due to rigid
covalent geometry. Additional details can be found in tamd.info.
Ref. J. Chen, W. Im and C. L. Brooks III, J. Comp. Chem. 2005, 26,
1565-1578.
rush: A simple implicit-solvent protein force-field that adds terms to
the bonded portion (bond + angle + dihe + impr + urey) of the all-atom
the hydrophobic effect (_U_nburied _S_urface), and intra-molecular and
protein-solvent hydrogen-bonding (_H_ydrogen-bonding) (hence _R_ _U_
_S_ _H_). Usage instructions are in doc/rush.info
gbsw: Optimized protein backbone parameters (par_all22_prot_gbsw.inp)
and atomic input radii (radius_gbsw.str) for a balanced GBSW implicit
solvent force field. The backbone phi/psi cross-term (CMAP) and the
atomic input radii have been re-optimized specifically to balance the
solvation and intramolecular interactions and to capture experimental
conformational equilibria of both helical peptides and
beta-hairpins. Additional information can be found in gbsw.info.
Ref. J. Chen, W. Im and C. L. Brooks III, J. Am. Chem. Soc. 128,
3728-36 (2006).
Description of topology and parameter files prior to version c31.
These files can be accessed via the toppar_history subdirectory of the
toppar directory.
(A) Topology files
top_all22_prot.inp all hydrogen RTF for proteins
top_all22_model.inp all hydrogen RTF for protein model cmpds
top_all22_sugar.rtf all hydrogen RTF for sugars
top_all27_na.rtf all hydrogen RTF for nucleic acids
top_all27_lipid.rtf all hydrogen RTF for lipids
top_all27_na_lipid.rtf all hydrogen RTF for nucleic acids and lipids
top_all27_prot_na.rtf all hydrogen RTF for proteins and nucleic acids
top_all27_prot_lipid.rtf all hydrogen RTF for proteins and lipids
toph19.inp extended atom RTF for proteins
toprna10r_22.inp extended atom RTF for nucleic acids
(B) Parameter files
par_all22_prot.inp all hydrogen parameters for proteins
par_all22_sugar.prm all hydrogen parameters for sugars
par_all27_na.prm all hydrogen parameters for nucleic acids
par_all27_lipid.prm all hydrogen parameters for lipids
par_all27_na_lipid.prm all hydrogen parameters for nucleic acids and lipids
par_all27_prot_na.prm all hydrogen parameters for proteins and nucleic acids
par_all27_prot_lipid.prm all hydrogen parameters for proteins and lipids
param19.inp extended atom parameters for proteins
pardna10_22.inp extended atom parameters for nucleic acids
par_hbond.inp hydrogen bond parameters for analysis only
Phased out: The CHARMM22 all-atom nucleic acid and lipid topology and
parameter files are no longer included in the toppar directory due to
their becoming obsolete. Note that they are included in the
toppar_history directories.
The CHARMM all-hydrogen topology and parameter sets may be
considered to be stable, however, minor bug fixes may be performed as
required. Additions may also occur leading to an expanding set of
parameters which are compatible across proteins, nucleic acids,
lipids, and, ultimately, carbohydrates. The carbohydrate(sugar)
parameter work is still in progress by John Brady and coworkers; the
number of sugar types should expand in the future. See the file
toppar_all.history for a listing changes in the files over time.
top_all22_model.inp includes the majority of model compounds used in
the protein parameterization and is to be used in conjunction with
par_all22_prot.inp.
Three sets of combined topology and parameter files are included
for use with 1) proteins and nucleic acids, 2) protein and lipids
and 3) nucleic acids and lipids. In all cases the CHARMM22 protein
parameters and the CHARMM27 nucleic acid or lipid parameters are
used. The designation all27 for these files is based on the
use of the most recent nucleic acid or lipid parameters. Test
calculations using these combined files have yielded good results.
Added as of July 1997 was the parameter file par_hbond.inp, which has
been renamed to stream/toppar_hbond.str. This file is included for
the analysis of hydrogen bonds; it includes information to calculate
h-bond energies, but these are basically meaningless. The hydrogen
bonds should NOT be used for energy, minimization and dynamics
calculations with the CHARMM all-hydrogen topology and parameter sets.
Ions in the all22 files are from two sources. Mg and Ca are from
Prodhom and Karplus and were optimized specifically for the all22
parameters. The remaining cations are from Benoit Roux (see his
thesis). They were optimized to be consistent with Param19, however,
MD studies in a number of groups have shown them to work well. Note
the presence of a variety of NBFIXES for the ions. These were
initially optimized based on the proteins and later transferred to the
lipids and nucleic acids based on analogy (by ADM Jr.). Ions in the
all27 files have been optimized based on free energies of solvation
by Roux and coworkers. As of August 1999 there were no NBFIXes
used with these ions.
The extended atom parameters for proteins are the same as those
included with CHARMM20 which are based on Wally Reiher's thesis. They
have been included in the supplement material of a recent publication
(see suggested citations below). For the extended atom nucleic acid
parameters those of Nilsson and Karplus, J. Comp. Chem. 7:591-616,
1986 are used which were also included in the CHARMM20 release and are
the only set to include explicit hydrogen bonding terms. Some
alterations of the extended atom nucleic acid topology and parameter
files have been made in order to maintain compatibility with the
multiple dihedral scheme in CHARMM22.
Please send all remarks and suggestions to the CHARMM web page at
www.charmm.org, Parameter Set Discussion Forum
ADM Jr., July 2008
www.charmm.org or
http://www.pharmacy.umaryland.edu/faculty/amackere/
References
EXTENDED ATOM NUCLEIC ACID PARAMETERS
Nilsson, L. and Karplus,M. Empirical Energy Functions for Energy
Minimizations and Dynamics of Nucleic Acids J. Comp. Chem.
7:591-616, 1986
PARAM19 PROTEIN PARAMETERS
Reiher, III., W.E. Theoretical Studies of Hydrogen Bonding, Ph.D.
Thesis, Department of Chemistry, Harvard University, Cambridge, MA,
USA, 1985
and
Neria, E., Fischer, S., and Karplus, M. Simulation of Activation Free
Energies in Molecular Systems, Journal of Chemical Physics, 1996, 105:
1902-21.
MacKerell, J., A.D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R. L.;
Evanseck, J.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.;
Joseph, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.;
Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, I., W. E.;
Roux, B.; Schlenkrich, M.; Smith, J.; Stote, R.; Straub, J.; Watanabe,
M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-hydrogen
Empirical Potential for Molecular Modeling and Dynamics Studies of
Proteins using the CHARMM22 Force Field. Journal of Physical
Chemistry B, 1998, 102, 3586-3616.
CMAP 2D correction surface
MacKerell, A.D., Jr,. Feig, M., Brooks, C.L., III, Extending the
treatment of backbone energetics in protein force fields: limitations
of gas-phase quantum mechanics in reproducing protein conformational
distributions in molecular dynamics simulations, Journal of
Computational Chemistry, 25: 1400-1415, 2004.
FOR PHOSPHOTYROSINE
Feng, M.-H., Philippopoulos, M., MacKerell, Jr., A.D., and Lim, C.
Structural Characterization of the Phosphotyrosine Binding Region of a
High-Affinity SH2 Domain-Phosphopeptide Complex by Molecular Dynamics
Simulation and Chemical Shift Calculations, Journal of the American
Chemical Society, 1996, 118: 11265-11277
Foloppe, N. and MacKerell, Jr., A.D. "All-Atom Empirical Force Field for
Nucleic Acids: 2) Parameter Optimization Based on Small Molecule and
Condensed Phase Macromolecular Target Data. 2000, 21: 86-104.
MacKerell, Jr., A.D. and Banavali, N. "All-Atom Empirical Force Field for
Nucleic Acids: 2) Application to Molecular Dynamics Simulations of DNA
and RNA in Solution. 2000, 21: 105-120.
Feller, S. and MacKerell, Jr., A.D. An Improved Empirical Potential
Energy Function for Molecular Simulations of Phospholipids, Journal
of Physical Chemistry B, 2000, 104: 7510-7515.
Feller, S. and MacKerell, Jr., A.D. An Improved Empirical Potential
Energy Function for Molecular Simulations of Phospholipids, Journal
of Physical Chemistry B, 2000, 104: 7510-7515.
Klauda, J.B., Brooks, B.R., MacKerell, A.D., Jr., Richard M. Venable,
R.M. and Pastor, R.W., An Ab Initio Study on the Torsional Surface of
Alkanes and its Effect on Molecular Simulations of Alkanes and a DPPC
Bilayer, Journal of Physical Chemistry B, 109; 5300- 5311, 2005
!above references and personal communication from the following
Jeffery Klauda
Joseph O'Connor
Marcus Hadle
Richard Venable
J. Alfredo Freites
Douglas Tobias
Carlos Mondragon-Ramirez
Igor Vorobyov
Alexander D. MacKerell, Jr
Richard W. Pastor
POLYUNSATURATED LIPIDS
Feller, S.E., Gawrisch, K. and MacKerell, Jr., A.D. "Polyunsaturated
Fatty Acids in Lipid Bilayers: Intrinsic and Environmental
Contributions to their Unique Physical Properties,: Journal of the
American Chemical Society, 2002, 124:318-326
NAD+, NADH and PPI
Pavelites, J.J., Bash, P.A., Gao, J. and MacKerell, Jr., A.D. A
Molecular Mechanics Force Field for NAD+, NADH, and the Pyrophosphate
Groups of Nucleotides, Journal of Computational Chemistry, 1997, 18:
221-239.
MacKerell Jr., A.D., Wiorkiewicz-Kuczera, J. and Karplus, M. An
all-atom empirical energy function for the simulation of nucleic
acids, Journal of the American Chemical Society, 1995,
117:11946-11975.
Patel, S., MacKerell, A.D., Jr., Brooks, C.L., III, CHARMM fluctuating
charge force field for proteins: II Protein/solvent properties from
molecular dynamics simulations using a nonadditive electrostatic
model, Journal of Computational Chemistry, 25: 1504-1514, 2004
Vorobyov, I., Anisimov, V.M., Greene, S., Venable, R.M., Moser, A.,
Pastor, R.W., and MacKerell, A.D., Jr. "Additive and Classical Drude
Polarizable Force Fields for Linear and Cyclic Ethers," Journal of
Chemical Theory and Computing, 3: 1120-1133, 2007
! O-C-C-O torsion modified
Hwankyu Lee, Richard M Venable, Alexander D MacKerell Jr., Richard W Pastor
Molecular dynamics studies of polyethylene oxide and polyethylene glycol:
Hydrodynamic radius and shape anisotropy
Biophysical J., 95: 1590-1599, 2008
! pyranose monosaccharides
Guvench, O., Greene, S.N., Kamath, G., Brady, J.W., Venable, R.M.,
Pastor, R.W., MacKerell, Jr., A.D. “Additive empirical force field for
hexopyranose monosaccharides†Journal of Computational Chemistry, 29:
2543-2564, 2008. PMID: 18470966
! linear sugars, sugar alcohols, and inositol
Hatcher, E., Guvench, O., and MacKerell, Jr., A.D. “CHARMM Additive
All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates
and Inositol,†Journal of Chemical Theory and Computation, 5:
1315-1327, 2009, DOI: 10.1021/ct9000608.
! hexopyranose glycosidic linkages
Guvench, O., Hatcher, E. R., Venable, R. M., Pastor, R. W., MacKerell,
A. D. Jr. “Additive Empirical CHARMM Force Field for glycosyl linked
hexopyranoses,†Journal of Chemical Theory and Computation, 5,
2353–2370, 2009, DOI: 10.1021/ct900242e
! furanose monosaccharides
Hatcher, E. R.; Guvench, O.; MacKerell, Hatcher, E., Guvench, O., and
MacKerell, Jr., A.D. “CHARMM Additive All-Atom Force Field for
Aldopentofuranose Carbohydrates and Fructofuranose.†Journal of
Physical Chemistry B. 113:12466-76, 2009, PMID: 19694450
!CHARMM GENERAL FORCE FIELD, CGenFF
Vanommeslaeghe, K., Hatcher, E.,Acharya, C., Kundu, S., Zhong, S.,
Shim, J., Darian, E., Guvench, O., Lopes, P., Vorobyov, I. and
Mackerell Jr., A.D., J. Comput. Chem., DOI: 10.1002/jcc.21367
Description of topology and parameter files in version c31 and
subsequent versions.
In version 31 a major restructuring of the topology and parameter
files was undertaken. This was performed to create a more modular
approach to the files, thereby avoiding the problem of files becoming
increasingly large. The restructuring was done such that the primary
topology and parameter files for biomolecules can be used as they were
previously. However, the topology and parameter information for the
majority of model compounds used in the parameter development,
additional molecules, including coenzymes, and patches parametrized to
be compatible with the CHARMM force fields have been moved to toppar
stream files. These toppar stream files have to be streamed in a
and parameter files. They include both the topology and parameter
information for the selected molecules, using the "read rtf card
append" and "read param card append" commands to append the additional
information to the topology and parameter lists. As of version c31 it
is still necessary to maintain all the MASS atom lists in the parent
topology and parameter files.
Files in Version C35/C36
Topology files
top_all22_prot.inp all hydrogen RTF for proteins, CHARMM22 with CMAP
top_all35_carb.rtf all hydrogen RTF for sugars
top_all32_lipid.rtf all hydrogen RTF for lipids with alkane dihedral update
top_all36_lipid.rtf all hydrogen RTF for lipids (C36 and on)
top_all27_na.rtf all hydrogen RTF for nucleic acids
top_all32_na_lipid.rtf all hydrogen RTF for nucleic acids and lipids
top_all36_na_lipid.rtf all hydrogen RTF for nucleic acids and lipids (C36 and on)
top_all27_prot_na.rtf all hydrogen RTF for proteins and nucleic acids
top_all32_prot_lipid.rtf all hydrogen RTF for proteins and lipids
top_all36_prot_lipid.rtf all hydrogen RTF for proteins and lipids (C36 and on)
top_all35_ethers.rtf all hydrogen RTF for ethers
top_all30_cheq_prot.inp all hydrogen RTF for protein charge equilibration polarizable model
toph19.inp extended atom RTF for proteins
toprna10r_22.inp extended atom RTF for nucleic acids
Parameter files
par_all22_prot.inp all hydrogen parameters for proteins with CMAP
par_all35_carb.prm all hydrogen parameters for sugars
par_all32_lipid.prm all hydrogen parameters for lipids with alkane dihedral update
par_all36_lipid.prm all hydrogen parameters for lipids (C36 and on)
par_all27_na.prm all hydrogen parameters for nucleic acids
par_all32_na_lipid.prm all hydrogen parameters for nucleic acids and lipids
par_all36_na_lipid.prm all hydrogen parameters for nucleic acids and lipids (C36 and on)
par_all27_prot_na.prm all hydrogen parameters for proteins and nucleic acids
par_all32_prot_lipid.prm all hydrogen parameters for proteins and lipids
par_all36_prot_lipid.prm all hydrogen parameters for proteins and lipids (C36 and on)
par_all30_cheq_prot.inp all hydrogen parameters for protein charge equilibration polarizable model
par_all35_ethers.prm all hydrogen parameters for ethers
param19.inp extended atom parameters for proteins
pardna10_22.inp extended atom parameters for nucleic acids
(C) Toppar stream files (see stream subdirectory) listed under the parent
topology and parameter files required for the individual files.
Parent files: can be used with prot, na and lipid files
toppar_dum_nobel_gases.str: dummy atom, helium and neon
toppar_hbond.str: stream file to estimate hydrogen bond interactions
Parent files: top_all22_prot.inp, par_all22_prot.inp
(or top_all22_prot_cmap.inp, par_all22_prot_cmap.inp)
toppar_all22_prot_model.str: model compounds used in protein parameter development
as well as additional compounds
toppar_all22_prot_aldehydes.str: small molecule aldehydes
toppar_all22_prot_aliphatic_c27.str: extends all22 protein force field to include
all27 alkane parameters
toppar_all22_prot_fluoro_alkanes.str: optimized fluoroalkanes, requires
toppar_all22_prot_aliphatic_c27.str
toppar_all22_prot_heme.str: heme, O2, CO, CO2 and related patches
toppar_all22_prot_pyridines.str: various substituted pyridines
toppar_all22_prot_retinol.str: retinol, model compounds, Schiff's bases
Parent files: top_all27_na.rtf, par_all27_na.prm
toppar_all27_na_model.str: model compounds used in na parameter development including
individual bases etc.
toppar_all27_na_base_modifications.str: various chemical modifications of bases
toppar_all27_na_carbocyclic.str: constrained bicyclic sugars
toppar_all27_na_nad_ppi.str: NAD, NADH, ADP, ATP and others. Useful in combination with
protein force field via the top_all27_prot_na.rtf
and par_all27_prot_na.prm
Parent files: top_all32_lipid.rtf, par_all32_lipid.prm
toppar_all27_lipid_model.str: model compounds used in lipid parameter development, including
alkenes
toppar_all27_lipid_cholesterol.str: cholesterol and related model compounds
Parent files: top_all36_lipid.rtf, par_all36_lipid.prm
toppar_all36_lipid_model.str: model compounds used in lipid parameter development, including
alkenes
toppar_all36_lipid_cholesterol.str: cholesterol and related model compounds
Parent files: top_all27_prot_na.rtf, par_all27_prot_na.prm
toppar_prot_na_all.str: all compounds that require both protein and nucleic acid toppar information
includes phosphorylated tyrosine, serine and threonine and some
coenzymes (SAH)
toppar_all27_na_bkb_modifications.str: various chemical modificaiton of the na backbone
including abasic variants and phosphoramidate
Parent files not needed
toppar_water_ions.str: contains TIP3P water model and ions. All of these
are also included in the prot, na and lipid topology
and parameter files.
toppar_amines.str: highly optimized neutral aliphatic amines.
(D) Parameters for the polarizable force field based on a classical
Drude oscillator. As this force field is currently under development
such that the parameters have been placed in the "drude" subdirectory.
Parameters for water, alkanes, ethers, aromatics, alcohols and amides
are available as of January 2007 and this list will be expanding. See
the 00readme for details and the approriate references.
(E) Parameters for selected silicate and aluminosilicate surfaces have
been developed. These parameters are designed to be compatible with
the CHARMM22 and 27 force fields allowing for biological
molecule-silicate surface interactions. As use of these parameters
requires creation of the surface, which entails creation of the
necessary patches, the parameters are included in the "silicates"
subdirectory. This directory also includes examples and code to
create the extended surfaces. See the 00readme file for more details.
ref: Lopes, P.E.M., Murashov, V. Tazi, M. Demchuk, E. MacKerell,
A. D., Jr. "Development of an Empirical Force Field for
Silica. Application to the Quartz-Water Interface," Journal of
Physical Chemistry B, 110: 2782-2792, 2006.
(F) Additional topology and parameter files from various sources are
included in subdirectories of the toppar directory. A description
follows:
non_charmm: Contains toppar files for AMBER, Bristol-Myers Squibb
(BMS) and OPLS force fields along with a stream file for the SPC and
SPC/E water models. These files have been tested to the extent that
they may be considered reliable representations of the original force
fields, though potentially not exact representations. These files are
NOT maintained and, thus, use at your own risk. See the 00readme
files and note that AMBER requires a special version of CHARMM as
described in the 00readme file.
tamdfff: An internal coordinate force field (ICFF) that was built
based on the CHARMM 22 protein force field. Specifically, it provides
a backbone covalent geometry suitable for torsion angle molecular
dynamics (TAMD) and the necessary CMAP cross-term corrections to
suppress distortions of the potential energy surface due to rigid
covalent geometry. Additional details can be found in tamd.info.
Ref. J. Chen, W. Im and C. L. Brooks III, J. Comp. Chem. 2005, 26,
1565-1578.
rush: A simple implicit-solvent protein force-field that adds terms to
the bonded portion (bond + angle + dihe + impr + urey) of the all-atom
the hydrophobic effect (_U_nburied _S_urface), and intra-molecular and
protein-solvent hydrogen-bonding (_H_ydrogen-bonding) (hence _R_ _U_
_S_ _H_). Usage instructions are in doc/rush.info
gbsw: Optimized protein backbone parameters (par_all22_prot_gbsw.inp)
and atomic input radii (radius_gbsw.str) for a balanced GBSW implicit
solvent force field. The backbone phi/psi cross-term (CMAP) and the
atomic input radii have been re-optimized specifically to balance the
solvation and intramolecular interactions and to capture experimental
conformational equilibria of both helical peptides and
beta-hairpins. Additional information can be found in gbsw.info.
Ref. J. Chen, W. Im and C. L. Brooks III, J. Am. Chem. Soc. 128,
3728-36 (2006).
Description of topology and parameter files prior to version c31.
These files can be accessed via the toppar_history subdirectory of the
toppar directory.
(A) Topology files
top_all22_prot.inp all hydrogen RTF for proteins
top_all22_model.inp all hydrogen RTF for protein model cmpds
top_all22_sugar.rtf all hydrogen RTF for sugars
top_all27_na.rtf all hydrogen RTF for nucleic acids
top_all27_lipid.rtf all hydrogen RTF for lipids
top_all27_na_lipid.rtf all hydrogen RTF for nucleic acids and lipids
top_all27_prot_na.rtf all hydrogen RTF for proteins and nucleic acids
top_all27_prot_lipid.rtf all hydrogen RTF for proteins and lipids
toph19.inp extended atom RTF for proteins
toprna10r_22.inp extended atom RTF for nucleic acids
(B) Parameter files
par_all22_prot.inp all hydrogen parameters for proteins
par_all22_sugar.prm all hydrogen parameters for sugars
par_all27_na.prm all hydrogen parameters for nucleic acids
par_all27_lipid.prm all hydrogen parameters for lipids
par_all27_na_lipid.prm all hydrogen parameters for nucleic acids and lipids
par_all27_prot_na.prm all hydrogen parameters for proteins and nucleic acids
par_all27_prot_lipid.prm all hydrogen parameters for proteins and lipids
param19.inp extended atom parameters for proteins
pardna10_22.inp extended atom parameters for nucleic acids
par_hbond.inp hydrogen bond parameters for analysis only
Phased out: The CHARMM22 all-atom nucleic acid and lipid topology and
parameter files are no longer included in the toppar directory due to
their becoming obsolete. Note that they are included in the
toppar_history directories.
The CHARMM all-hydrogen topology and parameter sets may be
considered to be stable, however, minor bug fixes may be performed as
required. Additions may also occur leading to an expanding set of
parameters which are compatible across proteins, nucleic acids,
lipids, and, ultimately, carbohydrates. The carbohydrate(sugar)
parameter work is still in progress by John Brady and coworkers; the
number of sugar types should expand in the future. See the file
toppar_all.history for a listing changes in the files over time.
top_all22_model.inp includes the majority of model compounds used in
the protein parameterization and is to be used in conjunction with
par_all22_prot.inp.
Three sets of combined topology and parameter files are included
for use with 1) proteins and nucleic acids, 2) protein and lipids
and 3) nucleic acids and lipids. In all cases the CHARMM22 protein
parameters and the CHARMM27 nucleic acid or lipid parameters are
used. The designation all27 for these files is based on the
use of the most recent nucleic acid or lipid parameters. Test
calculations using these combined files have yielded good results.
Added as of July 1997 was the parameter file par_hbond.inp, which has
been renamed to stream/toppar_hbond.str. This file is included for
the analysis of hydrogen bonds; it includes information to calculate
h-bond energies, but these are basically meaningless. The hydrogen
bonds should NOT be used for energy, minimization and dynamics
calculations with the CHARMM all-hydrogen topology and parameter sets.
Ions in the all22 files are from two sources. Mg and Ca are from
Prodhom and Karplus and were optimized specifically for the all22
parameters. The remaining cations are from Benoit Roux (see his
thesis). They were optimized to be consistent with Param19, however,
MD studies in a number of groups have shown them to work well. Note
the presence of a variety of NBFIXES for the ions. These were
initially optimized based on the proteins and later transferred to the
lipids and nucleic acids based on analogy (by ADM Jr.). Ions in the
all27 files have been optimized based on free energies of solvation
by Roux and coworkers. As of August 1999 there were no NBFIXes
used with these ions.
The extended atom parameters for proteins are the same as those
included with CHARMM20 which are based on Wally Reiher's thesis. They
have been included in the supplement material of a recent publication
(see suggested citations below). For the extended atom nucleic acid
parameters those of Nilsson and Karplus, J. Comp. Chem. 7:591-616,
1986 are used which were also included in the CHARMM20 release and are
the only set to include explicit hydrogen bonding terms. Some
alterations of the extended atom nucleic acid topology and parameter
files have been made in order to maintain compatibility with the
multiple dihedral scheme in CHARMM22.
Please send all remarks and suggestions to the CHARMM web page at
www.charmm.org, Parameter Set Discussion Forum
ADM Jr., July 2008
www.charmm.org or
http://www.pharmacy.umaryland.edu/faculty/amackere/
References
EXTENDED ATOM NUCLEIC ACID PARAMETERS
Nilsson, L. and Karplus,M. Empirical Energy Functions for Energy
Minimizations and Dynamics of Nucleic Acids J. Comp. Chem.
7:591-616, 1986
PARAM19 PROTEIN PARAMETERS
Reiher, III., W.E. Theoretical Studies of Hydrogen Bonding, Ph.D.
Thesis, Department of Chemistry, Harvard University, Cambridge, MA,
USA, 1985
and
Neria, E., Fischer, S., and Karplus, M. Simulation of Activation Free
Energies in Molecular Systems, Journal of Chemical Physics, 1996, 105:
1902-21.
MacKerell, J., A.D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R. L.;
Evanseck, J.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.;
Joseph, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.;
Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, I., W. E.;
Roux, B.; Schlenkrich, M.; Smith, J.; Stote, R.; Straub, J.; Watanabe,
M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-hydrogen
Empirical Potential for Molecular Modeling and Dynamics Studies of
Proteins using the CHARMM22 Force Field. Journal of Physical
Chemistry B, 1998, 102, 3586-3616.
CMAP 2D correction surface
MacKerell, A.D., Jr,. Feig, M., Brooks, C.L., III, Extending the
treatment of backbone energetics in protein force fields: limitations
of gas-phase quantum mechanics in reproducing protein conformational
distributions in molecular dynamics simulations, Journal of
Computational Chemistry, 25: 1400-1415, 2004.
FOR PHOSPHOTYROSINE
Feng, M.-H., Philippopoulos, M., MacKerell, Jr., A.D., and Lim, C.
Structural Characterization of the Phosphotyrosine Binding Region of a
High-Affinity SH2 Domain-Phosphopeptide Complex by Molecular Dynamics
Simulation and Chemical Shift Calculations, Journal of the American
Chemical Society, 1996, 118: 11265-11277
Foloppe, N. and MacKerell, Jr., A.D. "All-Atom Empirical Force Field for
Nucleic Acids: 2) Parameter Optimization Based on Small Molecule and
Condensed Phase Macromolecular Target Data. 2000, 21: 86-104.
MacKerell, Jr., A.D. and Banavali, N. "All-Atom Empirical Force Field for
Nucleic Acids: 2) Application to Molecular Dynamics Simulations of DNA
and RNA in Solution. 2000, 21: 105-120.
Feller, S. and MacKerell, Jr., A.D. An Improved Empirical Potential
Energy Function for Molecular Simulations of Phospholipids, Journal
of Physical Chemistry B, 2000, 104: 7510-7515.
Feller, S. and MacKerell, Jr., A.D. An Improved Empirical Potential
Energy Function for Molecular Simulations of Phospholipids, Journal
of Physical Chemistry B, 2000, 104: 7510-7515.
Klauda, J.B., Brooks, B.R., MacKerell, A.D., Jr., Richard M. Venable,
R.M. and Pastor, R.W., An Ab Initio Study on the Torsional Surface of
Alkanes and its Effect on Molecular Simulations of Alkanes and a DPPC
Bilayer, Journal of Physical Chemistry B, 109; 5300- 5311, 2005
!above references and personal communication from the following
Jeffery Klauda
Joseph O'Connor
Marcus Hadle
Richard Venable
J. Alfredo Freites
Douglas Tobias
Carlos Mondragon-Ramirez
Igor Vorobyov
Alexander D. MacKerell, Jr
Richard W. Pastor
POLYUNSATURATED LIPIDS
Feller, S.E., Gawrisch, K. and MacKerell, Jr., A.D. "Polyunsaturated
Fatty Acids in Lipid Bilayers: Intrinsic and Environmental
Contributions to their Unique Physical Properties,: Journal of the
American Chemical Society, 2002, 124:318-326
NAD+, NADH and PPI
Pavelites, J.J., Bash, P.A., Gao, J. and MacKerell, Jr., A.D. A
Molecular Mechanics Force Field for NAD+, NADH, and the Pyrophosphate
Groups of Nucleotides, Journal of Computational Chemistry, 1997, 18:
221-239.
MacKerell Jr., A.D., Wiorkiewicz-Kuczera, J. and Karplus, M. An
all-atom empirical energy function for the simulation of nucleic
acids, Journal of the American Chemical Society, 1995,
117:11946-11975.
Patel, S., MacKerell, A.D., Jr., Brooks, C.L., III, CHARMM fluctuating
charge force field for proteins: II Protein/solvent properties from
molecular dynamics simulations using a nonadditive electrostatic
model, Journal of Computational Chemistry, 25: 1504-1514, 2004
Vorobyov, I., Anisimov, V.M., Greene, S., Venable, R.M., Moser, A.,
Pastor, R.W., and MacKerell, A.D., Jr. "Additive and Classical Drude
Polarizable Force Fields for Linear and Cyclic Ethers," Journal of
Chemical Theory and Computing, 3: 1120-1133, 2007
! O-C-C-O torsion modified
Hwankyu Lee, Richard M Venable, Alexander D MacKerell Jr., Richard W Pastor
Molecular dynamics studies of polyethylene oxide and polyethylene glycol:
Hydrodynamic radius and shape anisotropy
Biophysical J., 95: 1590-1599, 2008
! pyranose monosaccharides
Guvench, O., Greene, S.N., Kamath, G., Brady, J.W., Venable, R.M.,
Pastor, R.W., MacKerell, Jr., A.D. “Additive empirical force field for
hexopyranose monosaccharides†Journal of Computational Chemistry, 29:
2543-2564, 2008. PMID: 18470966
! linear sugars, sugar alcohols, and inositol
Hatcher, E., Guvench, O., and MacKerell, Jr., A.D. “CHARMM Additive
All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates
and Inositol,†Journal of Chemical Theory and Computation, 5:
1315-1327, 2009, DOI: 10.1021/ct9000608.
! hexopyranose glycosidic linkages
Guvench, O., Hatcher, E. R., Venable, R. M., Pastor, R. W., MacKerell,
A. D. Jr. “Additive Empirical CHARMM Force Field for glycosyl linked
hexopyranoses,†Journal of Chemical Theory and Computation, 5,
2353–2370, 2009, DOI: 10.1021/ct900242e
! furanose monosaccharides
Hatcher, E. R.; Guvench, O.; MacKerell, Hatcher, E., Guvench, O., and
MacKerell, Jr., A.D. “CHARMM Additive All-Atom Force Field for
Aldopentofuranose Carbohydrates and Fructofuranose.†Journal of
Physical Chemistry B. 113:12466-76, 2009, PMID: 19694450
!CHARMM GENERAL FORCE FIELD, CGenFF
Vanommeslaeghe, K., Hatcher, E.,Acharya, C., Kundu, S., Zhong, S.,
Shim, J., Darian, E., Guvench, O., Lopes, P., Vorobyov, I. and
Mackerell Jr., A.D., J. Comput. Chem., DOI: 10.1002/jcc.21367